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pipeline:utilities:sxpipe_restacking [2018/08/07 22:05] moriya |
pipeline:utilities:sxpipe_restacking [2019/04/02 10:31] lusnig [See also] |
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~~NOTOC~~ | ~~NOTOC~~ | ||
- | ===== sxpipe | + | ===== sp_pipe |
- | Restacking: Generate all necessary information to restack the input stack (i.e. particle image ID list, CTF parameters list, projection parameters list) while appling micrograph selection list. Optionally, the command can directly output the virtual stack. | + | Restacking: Generate all necessary information to restack the input stack (i.e., particle image ID list, CTF parameters list, projection parameters list) while appling micrograph selection list. Optionally, the command can directly output the virtual stack. |
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Usage in command line | Usage in command line | ||
- | | + | |
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===== Typical usage ===== | ===== Typical usage ===== | ||
- | sxpipe | + | sp_pipe |
Do restacking to generate the virtual stack of only particle images associated to the micrographs in the selection list. | Do restacking to generate the virtual stack of only particle images associated to the micrographs in the selection list. | ||
- | | + | |
Generate the reboxing information of all particle images in the input stack. | Generate the reboxing information of all particle images in the input stack. | ||
- | | + | |
Generate the reboxing information of only particle images associated to the micrographs in the selection list. | Generate the reboxing information of only particle images associated to the micrographs in the selection list. | ||
- | | + | |
Do both restacking and reboxing to generate both the virtual stack and reboxing information of only particle images associated to the micrographs in the selection list. | Do both restacking and reboxing to generate both the virtual stack and reboxing information of only particle images associated to the micrographs in the selection list. | ||
- | | + | |
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===== Input ===== | ===== Input ===== | ||
=== Main Parameters === | === Main Parameters === | ||
- | ; input_bdb_stack_path : Input BDB image stack: Specify the input BDB image stack. (default required string) | + | ; input_bdb_stack_path : Input bdb image stack: Specify the input bdb image stack. (default required string) |
- | ; output_directory : Output directory: The results will be written here. This directory will be created automatically and it must not exist previously. (default required string) | + | ; output_directory : Output directory: The results will be written here. It cannot |
; %%--%%selection_list : Micrograph/ | ; %%--%%selection_list : Micrograph/ | ||
- | ; %%--%%shift3d_x : 3D x-shift [Pixels]: | + | ; %%--%%shift3d_x : 3D x-shift [Pixels]: 3D x-shift |
- | ; %%--%%shift3d_y : 3D y-shift [Pixels]: | + | ; %%--%%shift3d_y : 3D y-shift [Pixels]: 3D y-shift |
- | ; %%--%%shift3d_z : 3D z-shift [Pixels]: | + | ; %%--%%shift3d_z : 3D z-shift [Pixels]: 3D z-shift |
; %%--%%save_vstack : Save virtual stack: Use this option to save the virtual stack. By default, the virtual stack will not be generated. (default False) | ; %%--%%save_vstack : Save virtual stack: Use this option to save the virtual stack. By default, the virtual stack will not be generated. (default False) | ||
- | ; %%--%%sv_vstack_basename : Virtual stack basename: For %%--%%save_vstack, | + | ; %%--%%sv_vstack_basename : Virtual stack basename: For %%--%%save_vstack, |
; %%--%%reboxing : Generate reboxing information: | ; %%--%%reboxing : Generate reboxing information: | ||
- | ; %%--%%rb_box_size : Particle box size [Pixels]: For %%--%%reboxing option, specify the x and y dimensions of square area to be windowed. (default 0) | + | ; %%--%%rb_box_size : Particle box size [Pixels]: For %%--%%reboxing option, specify the x and y dimensions of square area to be windowed. (default 0) : %%--%%reboxing==True |
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=== List of output Files === | === List of output Files === | ||
|| **File Name** || **Discription** || | || **File Name** || **Discription** || | ||
- | || micrographs_in_input_stack.txt || Micrograph selection text file containing the list of micrograph basenames extracted from the input stack. This file can be used as micrograph selection text file of [[pipeline: | + | || micrographs_in_input_stack.txt || Micrograph selection text file containing the list of micrograph basenames extracted from the input stack. This file can be used as micrograph selection text file of [[pipeline: |
- | || micrographs_in_output_dataset.txt || Micrograph selection text file containing the list of micrograph in the output dataset. This file can be used as micrograph selection text file of [[pipeline: | + | || micrographs_in_output_dataset.txt || Micrograph selection text file containing the list of micrograph in the output dataset. This file can be used as micrograph selection text file of [[pipeline: |
|| input_stack_particle_id_for_output_dataset.txt || Particle selection text file containing the list of particle image IDs used for generating the output dataset from the input stack. This file can be used as particle selection list text file of [[pipeline: | || input_stack_particle_id_for_output_dataset.txt || Particle selection text file containing the list of particle image IDs used for generating the output dataset from the input stack. This file can be used as particle selection list text file of [[pipeline: | ||
- | || ctf_params_for_output_dataset.txt || CTF parameters text file containing CTF parameters of all particle images in the output dateset. This projection parameters can be used as inputs of [[pipeline: | + | || ctf_params_for_output_dataset.txt || CTF parameters text file containing CTF parameters of all particle images in the output dateset. This projection parameters can be used as inputs of [[pipeline: |
- | || original_proj_params_for_output_dataset.txt || Projection parameters text file containing **original** projection parameters of all particle images in the output dateset. This projection parameters can be imported to the reboxed stack using [[pipeline: | + | || original_proj_params_for_output_dataset.txt || Projection parameters text file containing **original** projection parameters of all particle images in the output dateset. This projection parameters can be imported to the reboxed stack using [[pipeline: |
- | || centered_proj_params_for_output_dataset.txt || Projection parameters text file containing **centered** projection parameters of all particle images in the output dateset. This projection parameters can be imported to the reboxed stack using [[pipeline: | + | || centered_proj_params_for_output_dataset.txt || Projection parameters text file containing **centered** projection parameters of all particle images in the output dateset. This projection parameters can be imported to the reboxed stack using [[pipeline: |
- | || original/ | + | || original/ |
- | || centered/ | + | || centered/ |
- | || EMAN2DB/ | + | || EMAN2DB/ |
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==== Files ==== | ==== Files ==== | ||
- | sparx/bin/sxpipe.py | + | sparx/bin/sp_pipe.py |
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==== See also ==== | ==== See also ==== | ||
- | [[pipeline: | + | [[pipeline: |
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